C1GALT1C1

C1GALT1 specific chaperone 1

Basic information

Region (hg38): X:120625673-120630054

Links

ENSG00000171155 ∙ NCBI:29071 ∙ OMIM:300611 ∙ HGNC:24338 ∙ Uniprot:Q96EU7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature	XL	Allergy/Immunology/Infectious; Cardiovascular; Hematologic; Renal	The condition can involve multi-systemic manifestations, and in addition to managing cardiovascular, infectious, hematologic, and renal complications, medical management (eg, with C5 inhibitor eculizumab) has been described as beneficial	Allergy/Immunology/Infectious; Cardiovascular; Craniofacial; Hematologic; Musculoskeletal; Neurologic	36599939; 37216524

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C1GALT1C1 gene.

• Polyagglutinable erythrocyte syndrome (19 variants)
• Inborn genetic diseases (7 variants)
• Hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature (2 variants)
• Atypical hemolytic-uremic syndrome (1 variants)
• Abnormal protein O-linked glycosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1GALT1C1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense	1	1	14	3	3	22
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	2	1	14	7	3

Variants in C1GALT1C1

This is a list of pathogenic ClinVar variants found in the C1GALT1C1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-120626227-C-G		Polyagglutinable erythrocyte syndrome • not specified	Uncertain significance (Jan 03, 2024)
X-120626273-T-C		Polyagglutinable erythrocyte syndrome	Likely benign (Nov 02, 2021)
X-120626404-T-C		not specified	Uncertain significance (May 30, 2023)
X-120626412-C-T		not specified	Uncertain significance (Jun 22, 2023)
X-120626501-C-G		Polyagglutinable erythrocyte syndrome • C1GALT1C1-related disorder	Likely benign (Jul 14, 2023)
X-120626505-T-C		Polyagglutinable erythrocyte syndrome	Uncertain significance (Aug 28, 2021)
X-120626531-C-T		Polyagglutinable erythrocyte syndrome	Likely benign (Jul 12, 2022)
X-120626561-A-T		Polyagglutinable erythrocyte syndrome • not specified	Uncertain significance (Dec 15, 2023)
X-120626570-G-C		not specified	Uncertain significance (Jan 26, 2022)
X-120626590-A-G		Polyagglutinable erythrocyte syndrome	Pathogenic (Aug 01, 2008)
X-120626627-A-C		Polyagglutinable erythrocyte syndrome	Pathogenic (-)
X-120626652-G-C		not specified	Uncertain significance (Aug 24, 2023)
X-120626654-G-T		not specified	Uncertain significance (May 08, 2023)
X-120626713-C-T		Polyagglutinable erythrocyte syndrome	Pathogenic (Oct 27, 2005)
X-120626726-C-T		Polyagglutinable erythrocyte syndrome	Likely benign (May 08, 2023)
X-120626727-G-A		Polyagglutinable erythrocyte syndrome	Likely benign (Jan 22, 2024)
X-120626737-G-A		Polyagglutinable erythrocyte syndrome	Uncertain significance (May 20, 2023)
X-120626739-G-A		Polyagglutinable erythrocyte syndrome	Benign (Jan 24, 2024)
X-120626774-A-T		Polyagglutinable erythrocyte syndrome • C1GALT1C1-related disorder	Benign/Likely benign (Jan 31, 2024)
X-120626776-C-T		not specified	Uncertain significance (Mar 29, 2022)
X-120626829-A-G		Polyagglutinable erythrocyte syndrome	Uncertain significance (Jan 04, 2023)
X-120626850-T-C		Polyagglutinable erythrocyte syndrome	Uncertain significance (Nov 27, 2023)
X-120626865-C-T		Polyagglutinable erythrocyte syndrome • C1GALT1C1-related disorder	Benign (Jan 22, 2024)
X-120626901-G-A		Atypical hemolytic-uremic syndrome • Hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature	Pathogenic (Jun 24, 2023)
X-120626951-A-G		Polyagglutinable erythrocyte syndrome	Likely benign (May 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1GALT1C1	protein_coding	protein_coding	ENST00000304661	1	4358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.852	0.146	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	84	115	0.730	0.00000798	2145
Missense in Polyphen		17	34.134	0.49804		672
Synonymous	0.0563	38	38.4	0.988	0.00000263	568
Loss of Function	2.32	0	6.26	0.00	4.50e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable chaperone required for the generation of 1 O- glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Probably acts as a specific molecular chaperone assisting the folding/stability of core 1 beta-3-galactosyltransferase (C1GALT1). {ECO:0000269|PubMed:12464682}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.259
• hipred: N
• hipred_score: 0.369
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: C1galt1c1
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: protein O-linked glycosylation;O-glycan processing, core 1;platelet activation;platelet morphogenesis
• Cellular component: Golgi membrane;integral component of membrane;extracellular exosome
• Molecular function: protein binding;glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity